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BGRS\SB-2014
Bioinformatics of Genome Regulation and Structure\Systems Biology
SYSTEM BIOLOGY SYMPOSIUM

PLENARY SESSION

Prof. Ruan Y. From 1D information to 3D genome structure and function
Prof. Rzhetsky A. Machine Science
Prof. Kaderali L. To be announced
Prof. Stepanov V.A. Adaptive evolution of genetic diversity and human diseases

EVOLUTIONARY BIOLOGY
Oral
Keynote talks

Liberles D. Lineage-Specific Processes of Genome Diversification

Oral presentations

Gunbin K.V., Afonnikov D.A. Selective shifts in recent evolution of Metazoa
Klimenko A. I., Matushkin Yu.G., Lashin S.A. Modeling evolution of spatially distributed bacterial communities simulation with Haploid Evolutionary Constructor
Naumoff D.G. Bioinformatic analysis of endo-beta-xylanases from Planctomycetes
Reva O., Korotetskiy I., Ilin A. Discovery of the role of horizontal gene exchange in evolution of pathogenic mycobacteria.
Sormacheva I.D., Smyshlyaev G.A., Blinov A.G. Transposable elements «flying» between lepidoptera species.
Zhong B. Streptophyte algae and the origin of land plants revisited using the chloroplast genomes and nuclear genes.

Poster

Bukin Y.S. Package of functions for script programming language R for testing the convergence of population samples of DNA sequences
Diallo A.B. A probabilistic framework for gene-tree reconstruction and reconciliation to a known species tree in the presence of duplication, loss and horizontal gene transfer
Gunbin K.V., Afonnikov D.A., Kolchanov N.A., Rogaev E.I., Derevianko A.P. Homo sapiens denisova craftsmanship can be related with evolution of the miRNAs regulating mRNAs
Gunbin K.V., Afonnikov D.A., Orlov Y.L. Molecular evolution of mammalian orthologous protein groups involved in stem cell specificity
Gunbin K.V., Afonnikov D.A. The relation between environmental changes and evolution of Archaea protein domains.
Gunbin K.V., Ponomarenko M.P., Afonnikov D.A., Gusev F., Rogaev E.I. What evolution of hominid TATA-boxes can tell us about human lineage?
Gunbin K.V. , Levitsky V.G., Vershinin A.V. What evolution of rye subtelomeric repeats can tell us about cereals speciations?
Katugina A.O., Kartavtsev Y.F. Comparative genetic analysis of three Far Eastern species of the genus Tribolodon according to sequence data of mitochondrial DNA CO-1 region.
Lashin S.A., Suslov V.V., Gunbin K.V. Forward-time simulation of evolutionary processes in ancient populations using the Diploid Evolutionary Constructor
Lenskiy S.V., Lenskaya T.I. Search for evolutional invariants by rank distribution of gene density in hominids
Maikova O.O., Sherbakov D.Yu., Belikov S.I. The two hypotheses of Baikal endemic sponge (Lubomirskiidae) evolution
Mustafin Z.S., Matushkin Yu.G., Lashin S.A. Allelic coadaptation and fitness landscape predetermine the optimal evolutionary mode in prokaryotic communities: a simulation study
Sherbakov D.Yu., Adelshin R.V., Anikin A.S., Gornov A.Yu. Methods of detection and estimation of evolutionary conserved elements of RNA secondary structure.
Borzov E.A., Mehta R., Baranova A.V., Skoblov M.Yu. Whole-genome comparative analysis of CpG islands between human and chimpanzee
Sokolov V.S., Gunbin K.V., Matushkin Y.G. Variation of elongation efficiency index of Archaea genes during evolution
Suslov V.V., Ponomarenko M.P., Gunbin K.V. Evolution of modern human and recombination of memes
Suslov V.V. Invasion, adaptation and evolution: when all out of sync
Suslov V.V., Safronova N.S., Orlov Y.L., Afonnikov D.A. The genomic text characteristics and GC content are related to the bacterial genome evolution
Turnaev I.I., Gunbin K.V., Akberdin I.R., Mironova V.V., Omelyanchuk N.A., Afonnikov D.A. Increasing the number of paralogs for enzymes involved in tryptophan biosynthesis during the evolution of land plants
Zverkov O.A., Seliverstov A.V., Lyubetsky V.A. A database of Rhodophyte plastid protein families and regulation of moeB genes

GENOMICS AND EPIGENETICS
Oral

Keynote talks

Nedoluzhko A.V., Boulygina E.S., Sokolov A.S., Tsygankova S.V., Schubert M., Gruzdeva N.M., Rezepkin A.D., Orlando L., Prokhortchouk E.B. De novo assembly of the mitochondrial genome of ~5000-year-old human from North Caucasus
Prof. Morozov A.V. Evidence for extensive nucleosome crowding in yeast chromatin
Chereji R.V., Kan T.-W., Guryev V.P., Morozov A.V., Moshkin Y.M. Biophysical principles guiding nucleosome positioning in vivo

Oral presentations

Antonov I.V., Marakhonov A.V., Baranova A., Skoblov M.Y. Prediction of antisense RNA-RNA interactions in animal cells
Babenko V.N. Transposons vs genes: survival strategies?
Djordjevic M. A biophysical approach to bacterial transcription start site prediction
Gunbin K.V., Popadin K.Y. 5’ and 3’ breakpoints of mtDNA deletions show drastic differences in dinucleotide properties
Ivashchenko A.T., Berillo O.A., Pyrkova A.Y., Niyazova R.E., Atambayeva S.A. The features of binding sites of miR-619-5p, miR-5095, miR-5096 and miR-5585-3p in the mRNAs of human genes
Golyshev M.A., Korotkov E.V. Computer annotation of bacterial genes using phylogenetic profiles
Krutinin G.G., Krutinina E.A., Kamzolova S.G., Osypov A.A. Electrostatic properties of bacteriophage lambda genome and its elements: virus vs host
Mitra C.K., Meena A.K. Association between microRNA and UTRs from human TLR genes
Oschepkov D.Y., Levitsky V.G., Kulakovskiy I.V., Ershov N.I., Makeev V.J., Merkulova T.I. Experimentally verified transcription factor binding sites models applied for computational analysis of ChIP-Seq data
Ryasik A.A., Grinevich A.A., Yakushevich L.V. Dynamics of nonlinear conformational excitations in functional regions of pttq18 plasmid
Subkhankulova T., Naumenko F. Is the single cell ChIP-Seq technique possible?
St. Laurent G., Shtokalo D., Tackett M.R., Nechkin S., Antonets D., Vyatkin Yu., Savva1 Y.A., Kapranov P., Lawrence C.E., and Reenan R.A. Whole genome analysis of A-to-I RNA editing using single molecule sequencing in Drosophila
Zharkov D. 5-methylcytosine and DNA oxidation: at the crossroads of epigenetics, DNA damage, and DNA repair

Poster

Alybaeva A.Z., Niyazova R.Y., Ivashchenko A.T. Binding sites of miRNA with MYB genes’ mRNA in B.taurus and B.mutus
Astakhova T.V., Tsitovich I.I., Yakovlev V.V., Roytberg M.A. Intron lengths and phases: regularities and database
Barducov N.V., Sipko T.P., Glazko V.I. Application of terminal Helitron fragments as high polymorphic markers of genome scanning in Ungulata
Baulin E.F., Spirin S.A., Roytberg M.A. Analysis and classification of nonstandard RNA motifs
Bogomolov A.G., Jetybayev I.E., Podkolodnyy N.L., Rubtsov N.B. Fluorescence in situ hybridization with microdissected DNA probes on chromosomes of species
Demenkov P.S., Ivanisenko V.A. Assembling genomes and metagenomes using cluster architecture
Drozdova P., Mironova L. Prionization of the Sfp1 protein in yeast does not mimic its inactivation at whole transcriptome level
Erkenov T.A. Application of multiloci genome scanning for identification of the Karachay horse genetic structure
Erokhin I.L. SINE-modeling of genome loop step
Gruzdeva N.M., Nedoluzhko A.V., Shulga O.A., Prokhortchouk E.B., Skryabin K.G. Novel microRNAs prediction in non-model organisms
Ignatieva E.V. Controlled vocabularies and information tables for the knowledge base on epigenetic control of human embryonic stem cells
Ignatieva E.V., Levitsky V.G., Kolchanov N.A. Functional characteristics of human genes containing low level of promoter polymorphism revealed from the 1000 Genomes Project dataset
Ivashchenko A.T., Berillo O.A., Pyrkova A.Y., Niyazova R.E. Features of interactions between miR-1273 family and mRNA of target genes
Korotkova A. Functional analysis of the promoter region of the Xist gene in mouse (Mus musculus)
Kulakova E.V., Bryzgalov L.O., Orlov Y.L., Li G., Ruan Y. Computer analysis of chromosome contacts revealed by sequencing
Kulakova E.V., Podkolodnaya O.A., Serov O.L., Orlov Y.L. Computer data analysis of genome sequencing by technology ChIP-seq and Hi-C
Levitsky V.G., Mironova V.V. The pipeline for composite regulatory elements prediction
Moskalev A.A., Plyusnina E.N., Peregudova D.O., Shaposhnikov M.V., Snezhkina A., Kudryavtseva A.V., Baranova A.M. Transcriptomics analysis of Drosophila melanogaster aging
Orazova S.B., Sagaydak A.I., Ivashchenko A.T. Interaction between miRNA and mRNA of MYB transcriptional factors family genes of maize
Osypov A.A. DEPPDB a portal for electrostatic and other physical properties of genome DNA
Osypov A.A. DNA phenotype and biophysical bioinformatics of transcription regulation in prokaryotes: the role of electrostatics as a natural selection factor
Krutinina E.A., Krutinin G.G., Kamzolova S.G., Osypov A.A. Transcription factors and electrostatic and other physical properties of their binding sites
Peregudova D.O., Plyusnina E.N., Shaposhnikov M.V., Kudryavtseva A.V., Snezhkina A.V., Moskalev A.A. Identification of Drosophila melanogaster genes as biosensors of chemical pollutants (formaldehyde, dioxin, toluene) and gamma-irradiation in low doses
Ponomareva N.S., Romanov D.E., Pshenichny E.A., Shkurat T.P. Scan elements in the non-coding DNA
Radchenko E.A., Tamazian G.S., Dobrynin P.V. Reference assisted chromosome assembly of 30 saccharomyces cerevisiae strains from saccharomyces genome database
Rusinov I.S., Ershova A.S., Karyagina A. S., Spirin S. A., Alexeevski V. Restriction sites avoidance is trace of lost restriction modification systems
Ryasik A.A., Temlyakova E. A., Sorokin A. A. Biological graph data base and its applications
Safronova N.S., Orlov Y.L. Computer analysis of human SNP containing sites by methods of text complexity estimations
Sergeev A.V., Temlyakova E.A., Sorokin A.A. Graph database for molecular biology: advantages of the graph representation of data
Sergeeva E.M., Koltunova M.K., Afonnikov D.A., Vasiliev G.V., Salina E.A. The structural organization and evolution of 5S rDNA of wheat chromosome 5BS by data of partial sequencing
Kondrakhin Yu., Valeev T., Sharipov R., Yevshin I. and Kolpakov F. Toolkit for ChIP-seq based comparative analysis of the PWM methods for prediction of transcription factor binding sites
Sokolov V.S., Zuraev B.S., Lashin S.A., Matushkin Yu.G. EloE a web-application for estimation of gene translation elongation efficiency in various organisms
Tan H., Hou X. SSRFace: an identification and search tool for genomic and transcriptomic SSR
Temlyakova E.A., Sorokin A.A. Graph analysis of E.coli transcription regulation
Vasiliev G.V., Gubanova N.V., Spitsina A.M., Safronova N.S., Orlov Y.L. Computer and experimental analysis of molecular mechanisms of gene expression regulation in brain tumor cells
Vishnevsky O.V. Analysis of the degenerate motifs in regions of binding sites of transcription factors essential for embryonic stem cells maintenance
Vishnevsky O.V., Kochetov A.V. Search for alternative translation starts in the genome of mycobacterium tuberculosis
Gluschenko O., Sharipov R. N., Kondrakhin Yu.V., Volkova O. A. The mRNA features important for translation initiation revealing using ribosome profiling data
Vorozheykin P.S., Titov I.I. Control of the miRNA pathways by the secondary structure and its account in the prediction tools

PLANTS SYSTEMS BIOLOGY
Oral

Keynote talk

Kapralov M.V., Whitney S.M. Evolution of RuBisCO encoding genes in plants and its implications for RuBisCO engineering in crops

Oral presentations

Afonnikov D.A., Genaev M.A., Komyshev E.G., Doroshkov A.V., Pshenichnikova T.A., Morozova E.V., Simonov A.V. Computer high-throughput approaches to wheat phenotyping
Doroshkov A.V., Zubairova U.S., Genaev M.A., Nikolaev S.V., Pshenichnikova T.A., Afonnikov D.A. Analysis of bread wheat leaf pubescence formation and diversity using image analysis technique and mathematical modeling
Kanayama Y., Ikeda H. Metabolome and transcriptome analyses of a tomato introgression line containing a Solanum pennellii chromosome segment
Karlov G.I., Divashuk M.G., Alexandrov O.S., Razumova O.V., Khuat T.M.L., Kroupin P.Yu. Plant molecular cytogenetics and next-generation sequencing data analysis
Kazantsev F.V., Chernova V.V., Doroshkov A.V. , Omelyanchuk N.A., Mironova V.V., Likhoshvai V.A. Self-organization mechanisms for auxin distribution in the root apical meristem
Pinsky I.V., Ivashchenko A.T. miRNAs binding to mRNAs of rice MYB genes
Ponomarenko P.M., Ponomarenko M.P. An empirical equilibrium equation of a gene response to auxin in plants allows to predict quantitatively the auxin response
Sergeeva E.M., Timonova E.M., Bildanova L.L., Koltunova M.K., Nesterov M.A., Magni F., Frenkel Z., Dolezel J., Faris J., Sourdille P., Feuillet C., Salina E.A. The progress in physical mapping of chromosome 5B of bread wheat Triticum aestivum
Sarsenbayev K.N. Proteomic information of spring wheat varieties differing in resistance to infection after Puccinia recondita inoculation

Posters

Dobrovolskaya O., Amagai Y., Pont C., Martinek P., Krasnikov A.A., Orlov Y.L., Salina E.A., Salse J., Watanabe N. Genetic dissection of the inflorescence branching trait in diploid, tetraploid and hexaploid wheats
Ikeda H., Kanayama Y. Analysis of a tomato introgression line, IL8-3, with increased Brix content using the whole-genome sequence
Komyshev E.G., Genaev M.A., Afonnikov D.A. SeedCounter — mobile and desktop application for high-throughput phenotyping seeds in wheat
Lavrekha V.V., Omelyanchuk N.A., Mironova V.V. Modeling of cell dynamics in the root apical meristem with Dynamical Grammar
Novoselova E.S., Mironova V.V., Kazantsev F.V., Omelyanchuk N.A, Likhoshvai V.A. Computation modeling of vascular patterning in plant roots
Perfilyeva A.I. The statistical analysis of level of an expression of a series of proteins of a plant of Arabidopsis thaliana in the conditions of stressful influence
Zubairova U.S., Nikolaev S.V., Doroshkov A.V., Afonnikov D.A. A model of trichome spacing pattern formation on growing wheat leaf
Zubairova U.S., Nikolaev S.V. A simple mechanical cell-based model for symplastic growth of linear leaf blade

PROTEOMICS, METABOLOMICS AND COMPUTATIONAL PHARMACOLOGY
Oral
Keynote talk

Larina I.M., Ivanisenko V.A., Nikolaev E.N. Proteomics extreme impacts as a tool for systems biology

Oral presentations

Aksianov E.A., Alexeevsky A.V. Alignment of “unalignable” protein structures
Anashkina A.A., Esipova N.G., Kuznetsov E.N., Tumanyan V.G. Native proteins and Decoys: subtle structure differences
Andrianov A.M., Kashyn I.A., Tuzikov A.V. Computational prediction of novel anti-HIV-1 agents based on potent and broad neutralizing antibody VRC01
Binder H., Wirth H., Arakelyan A., Lembcke K., Tiys E.S., Ivanishenko V., Kolchanov N.A., Kononikhin A., Popov I., Nikolaev E.N., Pastushkova L., Larina I.M. A machine learning analysis of urine proteomics in space-flight simulations
Chekmarev S.F. Driving force for protein folding: the two-component potential
Chugunov A.O., Volynsky P.E., Efremov R.G. High-performance computing provides insight into the innermost organization
Duzhak T., Tsentalovich Y. Lens cataract: effects of crystallins modification
Karpova M.A., Karpov D.A., Ivanov M.V., Zgoda V.G., Gorshkov M.V., Moshkovskii S.A. Cancer cell line recognition by shotgun proteomics using cancer exome data
Medvedev K.E., Afonnikov D.A. Computational investigation of high pressure and temperature influence
Mescheryakova I.A., Demidova E.V., Demidov E.A., Goryachkovskaya T.N., Popik V.M., Semenov A.I., Kulipanov G.N., Kolchanov N.A., Peltek S.E. Genomic proteimic profiling
Nyporko A.Y. Features 8-oxo-dGTP behavior in active site of human DNA polymerase
Pastushkova L.H., Kononihin A.S., Tiys E.S., Obraztsova O.A., Dobrohotov I.V., Kireev K.S., Ivanisenko V.A., Nikolaev E.N., Larina I. M. Identifying overrepresented biological processes in cosmonauts on the first day
Sherin P.S., Zelentsova E.A., Sormacheva E.D., Duzhak T.G., Tsentalovich Yu.P. UVA-induced modifications of lens alpha-crystallin

Poster

Fomin E.S., N.A. Alemasov L-MOLKERN software allowing for polarization effects in free energy calculation
Bragin A.O., Sokolov V.S., Demenkov P.S., Matushkin Yu.G., Ivanisenko V.A. Computer analysis of expression level of allergen-coding genes of pathogenic microorganisms
Davidovich P., Aksenova V., Martin S.J. Molecular dynamics structure modeling of IL-36 cytokines
Deeva A.A., Nemtseva E.V., Kratasyuk V.A. Spectral characterystics of tryptophan in water and Vibrio harveyi luciferase
Gurkov A.N., Kondratyeva E.M., Bedulina D.S. ImageJ addon for 2D electrophoresis gel analysis
Igolkina A.A., Samsonova M.G. Method to predict the percentage of cell types in human blood
Ivanisenko N.V., Tregubchak T.V., Saik O.V., Ivanisenko V.A. and Shchelkunov S.N. Molecular mechanisms of interaction of Tumor Necrosis Factor
Ivanisenko T.V., Demenkov P.S., Ivanisenko N.V., Ivanisenko V.A. New versions of the PDBSite database and PDBSiteScan tool_ prediction of functional sites in the protein 3d structure
Liu J., Kang X. Backbone encodings in protein stability predictions
Nizhnikov A.A., Antonets K.S., Inge-Vechtomov S.G. SARP: an algorithm for annotation of the compositionally biased regions in protein sequences
Orlov A.A., Osolodkin D.I., Palyulin V.A., Zefirov N.S. Analysis of the binding mode of antiviral peptides to the Flavivirus envelope protein E based on protein-protein docking
Raevsky A.V., Samofalova D.A., Кarpov P.A., Blume Y.B. Identification of potential inhibitor of protein kinase D1 (PKD1) and 2 (PKD2)
Tiys E.S., Demenkov P.S., Saik O.V., Popik O.V., Ivanisenko V.A. Reconstruction of associative gene networks specific to target biological processes and phenotypic traits
Yuldasheva G.A., Ilin A.I., Zhidomirov G.M. Enhancing anticancer activity of doxorubicin by molecular iodine complexes with bioactive organic ligands and lithium salts
Zanegina O.N., Karyagina A.S., Alexeevski A.V., Spirin S.A. Contact-based approach to structural classification of protein-DNA complexes

SYSTEMS COMPUTATIONAL BIOLOGY
Oral

Keynote talk

Binder M., Modelling of the Hepatitis C Virus Life Cycle
Ratushny A.V., Danziger S.A., Wurtmann E.J., Baliga N.S. and Aitchison J.D. Multiscale modeling as a framework for exploring molecular mechanisms of biological systems

Oral presentations

Akberdin I.R., Ermak T.V., Kazantsev F.V., Khlebodarova T. M. and Likhoshvai V.A. Kinetic modeling of pyrimidine biosynthesis is a first step to in silico bacterial cell
Akberdin I.R., Ivanisenko N.V., Oschepkova E.A., Omelyanchuk N.A., Matushkin Yu.G., Afonnikov D.A. and Kolchanov N.A. Regulatory mechanisms for mESC self-renewal: kinetic and stochastic modeling
Djordjevic M., Severinov K., and Djordjevic M. Modeling bacterial immune systems: CRISPR/CAS regulation
Duk M.A., Samsonov A.M., and Samsonova M.G. Mechanism of miRNA action defines the dynamical behavior of miRNA-mediated feed-forward loops
Hubert F., Honoré S., Petit M., Barlukova A. Dynamic instabilities of microtubules
Ivanisenko N., Mishchenko E., Akberdin I., Demenkov P., Kozlov K., Todorov D., Gursky V.V., Samsonova M.G., Samsonov A.M., Clausznitzer D., Kaderali L., Kolchanov N.A., and Ivanisenko V.A. Mathematical model for Subgenomic hepatitis C virus replication: impact of drug resistance
Kashina E.V., Oshchepkov D.Y., Oshchepkova E.A., Shilov A.G., Antontseva E.V., Furman D.P., Mordvinov V.A. Dioxin-mediated regulation of genes involved in cytokines production by macrophages
Kozlov K.N., Gursky V.V., Kulakovskiy I.V., Muzhichenko V.V. and Samsonova M.G. Sequence -based model of gap gene regulatory network
Kursanov A., Solovyova O., Katsnelson L., Medvedev K., Vasilyeva A., Vikulova N., Markhasin V.S. Cardiac mechanics, calcium overload and arrhythmogenesis
Narula J., Kuchina A., Süel G.M. and Igoshin O.A. Slowdown of cell growth acts as the signal triggering cellular differentiation
Popik O.V., Kolchanov N.A., Ivanisenko V.A. Mathematical modeling of the interactions between molecular genetic systems
Ryzhkov P.A., Ryzhkova N.S. Graph model of type I diabetes
Lashin S.A., Matushkin Yu.G. DEC: software tools for simulation evolution in diploid populations

Poster

Aksenova E.I., Voronina O.L., Kunda M.S., Semenov A.N., Zamyatnin A.A., Lunin V.G., Gintsburg A.L. Hidden reserves of used vaccine substrain
Likhoshvai V.A., Khlebodarova T.M., Bazhan S.I., Gainova I.A., Chereshnev V.A., Bocharov G.A. Tat-Rev regulation of HIV-1 replication: mathematical model predicts the existence of oscillatory dynamics
Ermak T.V., Akberdin I.R., Timonov V.S., Mischenko E.L., Oschepkova E.A., Perfilyeva O.A., Smirnova O.G., Khlebodarova T. M and Likhoshvai V.A. KiNET 1.0: a new web database on kinetics data and parameters for E. coli metabolic pathways
Galimzyanov A.V. GTML format for gene nets data representation
Ignatieva E.V. The knowledge base on molecular genetics mechanisms controlling human lipid metabolism
Kononenko L.I. Direct and inverse problems for systems with small parameter in kinetics models
Korla K. Kinetic simulation of mitochondrial shuttles
Lashin S.A., Klimenko A.I., Mustafin Z.S., Chekantsev A.D., Zudin R.K., Matushkin Yu.G. Haploid Evolutionary Constructor 3D: a tool for simulation of spatially distributed prokaryotic communities
Mikhaelis M., Chernyshev A.V., Yurkin M.A., Nekrasov V.M. and Maltsev V.P. Apoptotic nuclear volume decrease: analysis of confocal images and mathematical model
Oschepkova E.A., Omelyanchuk N.A., Akberdin I.R., Ermak T., Afonnikov D.A. Database of quantitative characters of processes in embryonic stem cells
Perfilyeva O.A., Likhoshvai V.A., Khlebodarova T.M. Mathematical modeling of peptidoglycan precursor biosynthesis in the cytoplasm of Esherichia coli cell
Podkolodnaya O.A., Podkolodnaya N.N., Podkolodnyy N.L. The mammalian circadian clock: computer analysis of gene network
Popik O.V., Arkova O.V., Rasskazov D.A., Saik O.V., Ponomarenko P.M., Arshinova T.V., Savinkova L.K, Ponomarenko M.P. and Kolchanov N.A. Annotations of SNPs in promoters of human oncogenes VEGFA, EGFR, ERBB2, IGF1R, VEGFR1(2) AND HGFR
Popik O.V., Hofestaedt R., Ivanisenko V.A. Evaluation of pathways efficiency based on data on ppi and distribution of proteins over cellular localizations
Ri M.T., Wölfl S., Zakhartsev M. Experimental data for testing the adequacy of existing mathematical models
Ri M.T., Saik O.V., Khayrulin S.S. The mathematical model of Rob, MarR, MarA regulatory circuit of Escherichia coli gene network
Ilin A., Islamov R., Kasenov S., Nurseitov D., Serovajsky S. Mathematical modeling of lung infection and antibiotic resistance
Shamanina M. Putative candidate genes transcriptionally upregulated both in acute and chronic phase of response
Shlikht A.G., Kramorenko N.V. Integrated genome-oriented information system for monitoring and control of biological systems
Spitsina A.M., Efimov V.M., Babenko V.N., Orlov Y.L. Computer analysis of human gene expression data using BioGPS database of microarray Affymetrix U133
Stepanenko I.L., Ivanisenko V.A. Logical modelling of Nanog-depended transcriptional gene network of embyonic carcinoma stem cells
Yuldasheva G.A., Ilin A.I., Zhidomirov G.M. Lithium halides enhance the anticancer activity of cisplatin
Zhabereva A.S., Gainullin M.R., Ivanchenko M.V., Kel A.E. Global mapping of protein ubiquitylation within TNF-alpha signaling pathway using geneXplain platform

ISHG-2014
SYMPOSIUM “HUMAN GENETICS”

MEDICAL GENETICS
Oral

Keynote talks

Polyakov A. To be announced
Maksimov V. Personalized genomic medicine: today and prospects
Khusnutdinova E. Diversity of mitochondrial DNA haplogroup among the peoples of Eastern Europe

Oral presentations

Bragina E., Freidin M., Tiys E., Koneva L., Ivanisenko V., Puzyrev V. Genome-phenome relationships of polar immunological diseases
Bryzgalov L., Brusentsov I., Merkulova T. A novel approach to functional SNP discovery from genome-wide data reveals new variants, associated with colon cancer risk
Golubenko M., Salakhov R., Makeeva O., Kashtalap V., Barbarash O., Puzyrev V. Analysis of mitochondrial DNA polymorphism in patients with acute coronary syndrome
Goncharova I., Makeeva O., Tarasenko N., Markov A., Buikin S., Puzyrev V. Molecular genetic peculiarities of fibrogenesis in different pathological traits in humans
Goncharova R., Nikitchenko N., Ramaniuk V., Savina N., Kuzhir T. XPD, XRCC1, OGG1 and ERCC6 polymorphisms and human lifespan
Gusar V.A. Evaluation of differential miRNA expression after permanent focal ischemia in rat brain using real-time qRT-PCR and NGS
Kharkov V.N., Radzhabov M.O. Stepanov V.A. Gene pool of the native populations of Dagestan: territorial subdivision and correlation with linguistic classification from the data of Y-chromosome markers
Lebedev I.N., Kashevarova A.A., Skryabin N.A. Genome architecture and chromosomal diseases
Lenskiy S.V., Lenskaya Y. Relationships between human gene set and set of gene disorders
Nazarenko M., Markov A., Sleptcov A., Lebedev I., Skryabin N., Kashevarova A., Frolov A., Barbarash O., Puzyrev V. Genome-wide profiling of DNA copy number and methylation in atherosclerosis
Ponomarenko M., Arkova O., Saik O., Arshinova T., Ponomarenko P., Rasskazov D., Genaev M., Komyshev E.G, Savinkova L., Kolchanov N.A. Annotations in silico of 388 SNPs of the core-promoters of 68 human feeding behavior genes
Posukh O., Сhurbanov A., Karafet T., Bondar A., Morozov I., Mikhalskaya V., Zytsar M. Whole exome sequencing in Altaian families (the Altai Republic, Southern Siberia) with congenital hearing loss
Sharapov S., Tsepilov Y., Ried J., Strauch K., Gieger C., Aulchenko Y. Genome-wide environmental sensitivity analysis of human metabolomics data
Skryabin N.A., Lebedev I.N. Somatic genome variability and morphological heterogeneity of breast cancer
Timofeeva A., Gusar V., Shram S., Zhanin I., Snezhkina A., Kudryavtseva A., Serenko A.A., Pinelis V., and Bobrov M. Comparative NGS analysis of miRNA expression in rat brain and blood plasma after transient focal ischemia
Trifonova E., Ershov N., Serebrova V., Stepanov V. Identification of new genetic markers for preeclampsia using an integrated approach
Yudin N., Mishakova T., Maksimov V., Gafarov V., Malyutina2 S., Voevoda M. Association of the dopamine receptor D4 (DRD4) gene polymorphism with cardiovascular disease risk factors

Poster

Astrakova K.S., Shakhtshneider E.V., Ragino Y.I, Chernjavski A.M., Kashtanova E.V., Polonskaya Y.V., Voevoda M.I. Cholesterol ester transfer protein gene polymorphism in men with coronary atherosclerosis.
Babushkina N.P., Garaeva A.F., Bragina E.Yu., Nogovitsina A.N., Rudko A.A. Studying of genes regulating immune response at pulmonary tuberculosis in Yakuts_
Eslami G., Hajimohammadi B., Gholamrezaei M., Khalatbary S., Zohortabar A., Ardian M. Practical approach for DNA extraction of Linguatula serrata nymphs: an analytical method
Garaeva A.F., Rudko A.A., Bragina E.Yu., Babushkina N.P., Freidin M.B. Study of genes causing atypical familial mycobateriosis in Tomsk tuberculosis patients
Ibeh B.O. CCR5 and CXCR4 coreceptor profile in resistance HIV exposed but seronegative individuals of Nigerian origin
Ivanoshchuk D.E., Konovalova N.A., Bychkov I.Y., Konovalova O.S., Eremina A.V., Ponomareva M.N., Voevoda M.I., Romaschenko A.G. Possible association between the TRPV1 gene rs222747 polymorphism and primary open angle glaucoma in western Siberia patients
Ivanova A.A., Maksimov V.N., Orlov P.S., Ivanoshchuk D.E., Savchenko S.V., Voevoda M.I. Association of the genetic markers for myocardial infarction with sudden cardiac death in a Russian population
Koneva L.A, Freidin M. B., Bragina E.Yu., Puzyrev V.P, McEachin R.C Modeling genetic influences on two diseases that are unusually rare in co-occurrence: bronchial asthma and pulmonary tuberculosis
Korbolina E.E., Ershov N.I., Bryzgalov L.O., Kozhevnikova O.S., Kolosova N.G. Congenic strains for studying accelerated senescence in OXYS rats: retinal transcriptome and candidate gene analysis by RNASeq
Podkolodnyy N.L., Afonnikov D.A., Vaskin Yu.Yu., Bryzgalov L.O., Ivanisenko V.A., Demenkov P.S., Ponomarenko M.P., Rasskazov D.A., Gunbin K.V., Protsyuk I., Shutov I., Leontyev P., Fursov M.Yu., Bondar N.P., Antontseva E.V., Merkulova T.I., Kolchanov N.A. The SNP-MED system for personal medicine_ analyze the effect SNP to the function of genes associated with diseases
Sergeev R.S., Kavaliou I.S., Tuzikov A.V. Mutation analysis of Mycobacterium Tuberculosis genome and association with drug resistance
Vechkapova S.O. Intermolecular interactions in the ionotropic glutamate receptor supramolecular complexes in the processes of neuronal synaptic plasticity
Voropaeva E.N., Pospelova T.I., Voevoda M.I., Maximov V.N. Polymorphism rs1625895 gene tp53 and effectiveness of treatment of DLBCL

TRANSLATIONAL MEDICINE
Oral

Keynote talks

Iwakura Y. The role of DECTIN-1 and DECTIN-2 in the host defense against fungi and in intestinal immunity
Brown S. Mechanisms of circadian plasticity

Oral presentations

Baranova A., Wang L., Cui T., Veytsman B., Bruskin S. Attractor based classifiers for prediction of post-treatment survival in cancer and detection of non-malignant diseases
Erokhin I.L. Oncogenesis model based on the genome structure of multicellular organisms
Grinkevich L.N. Epigenetic mechanisms of memory formation: the role of the histone acetylation and methylation in aversive learning
Kozhevnikova E. Gut mucosal proteoglycan Mucin2 compromises animal sexual behavior
Medvedev S.P. The use of new genome engineering technologies for creation of isogenic amyotrophic lateral sclerosis cell model
Menshanov P.N., Akulov A.E., Dygalo N.N. Hippocampal neurochemical profile in neonatal rats: effects of anesthesia
Nemudryi A.A. Rescue of Brattleboro rat strain mutant phenotype using TALEN and CRISPR/Cas9 systems
Pakharukova M.Y., Ershov N.I., Pirozhkova D.S., Vavilin V.A., Zadesenets K.S., Duzhak T.G., Mordvinov V.A. Molecular mechanisms of metabolism, excretion and drug tolerance in human liver fluke Opisthorchis felineus
Pozhilenkova E. Development of cellular models for translational research in neuropharmacology
Redina O.E., Smolenskaya S.E., Abramova T.O., Ivanova L.N., Markel A.L. Genetic dissection of inherited hypertensive state in ISIAH rats using kidney gene-expression and genome mapping
Salmina A.B., Malinovskaya N.A., Lopatina O.L., Khomleva Y.K. Molecular markers and targets for diagnostics and treatment of neurodegeneration and neurodevelopmental disorders
Stefanova N.A., Muraleva N.A., Strunov A.A., Kiseleva E.V., Kolosova N.G. The senescence-accelerated OXYS rats as a model of Alzheimer disease
Telegina D.V., Kozhevnikova O.S., Baiborodin S.I., Kolosova N.G. Alterations of rat retinal pigment epithelium with age and AMD-like retinopathy
Veytsman B., Cui T., Wang L., Baranova A. Systemic shifts in micro RNA landscape as a diagnostic and prediction tool

Posters

Avetisyan A.V., Simonyan R.A., Aleksandrova I.Ju, Samokhin A.N., Bobkova N.V. Mitochondrial disfunctions in animal model of sporadic Alzheimer’s disease
Astrakova K.S. — CHOLESTEROL ESTER TRANSFER PROTEIN GENE POLYMORPHISM IN MEN WITH CORONARY ATHEROSCLEROSIS
Bondar N.P., Bryzgalov L.O., Ershov N.I., Matveeva M.Yu. The use of 3D-chromatin structure data to predict novel genes associated with the development of depression
A.G. Galyamina, I.L. Kovalenko, N. N. Kudryavtseva Relationship between anxiety and depression in the chronic social defeat stress model: pharmacological research
Ignatieva E.V. The compellation of human genes controlling feeding behavior or associated with body mass index and its functional and genomic characteristics
Kovalenko I.L., Galyamina A.G., Smagin D.A., Michurina T.V., Enikolopov G., Kudryavtseva N.N. Implications of hostile environment and social instability in adolescent mice
Kozhevnikova O.S., Korbolina E.E., Ershov N.I., Kolosova N.G. Aging of rat retina: transcriptome study
Medvedeva I.V., Spitsina A.M., Vishnevsky O.V., Safronova N.S., Efimov V.M., Orlov Y.L. Computer analysis of human gene expression data in brain using microarrays
Muraleva N., Kozhevnikova O., Korbolina E., Fursova A., Kolosova N. Estimation of impact of alpha-crystallin’s alterations on the development of AMD-like retinopathy in OXYS rats
Perepechaeva M.L., Kolosova N.G., Grishanova A.Yu. AhR-dependent genes CYP1B1 and CYP2J3 are involve in cardiovascular pathology of senescence-accelerated OXYS rats
Rudnitskaya E.A., Maksimova K.Y., Stefanova N.A. Melatonin in prevention of Alzheimer’s disease-like pathology in OXYS rats
Salyakina D., Tsinoremas N.F. Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data
Shvarev Y.N., Demenkov P.S., Balakireva O.M., Ivanisenko V.A., Kolchanov N.A. Can opioid and substance p system interaction antogonize morphine-induced respiratory depression?
Smagin D.A., Kudryavtseva N.N., Enikolopov G.N. Activation of hippocampal cell proliferation and decrease of c-fos expression in the amygdala under positive fighting experience in male mice
Vitovtov A.O., Muraleva N.A., Stefanova N.A., Kolosova N.G. Conservative mTOR signaling pathway as a target for prophylaxis of accelerated brain aging

MM-HPC-BBB-2014
INTERANTIONAL CONFERENCE MATHEMATICAL MODELING AND HIGH PERFORMANCE COMPUTING IN BIOINFORMATICS,
BIOMEDICINE AND BIOTECHNOLOGY

MATHEMATICAL MODELING IN BIOMEDICINE AND HIGH-PERFORMANCE COMPUTING IN BIOINFORMATICS
Oral

Keynote talk

Chupakhin A.P., Cherevko A., Khe A., Chebotnikov A., Krivoshapkin A., Orlov K., Panarin V. Comprehensive study of hemodynamics of cerebral vessels in the presence of pathologies
Asmanova N., Koloskov G., Ilin A.I. On the application of excretion data as a criteria of choice between multiple solutions of inverse problem in pharmacokinetics
Ayupova N.B., Golubyatnikov V.P. On geometry of phase portraits of some low-dimensional gene network models
Akinshin A.A., Bukharina T.A., Furman D.P., Golubyatnikov V.P. Modeling of two-cells complex in morphogenesis of D. melanogaster mechanoreceptors
Mikhailenko B.G., Glinskiy B.M., Kuchin N.V., Chernykh I.G. Siberian supercomputer center as a service for bioinformatics
Ilyin A.I., Kabanikhin S.I., Krivorotko O.I., Voronov D.A. Inverse problems for differential equations of pharmacokinetics and immunology

Oral presentations

Afanasyev I.V. Application of cellular automata for investigation of pollution influence on Macrohectopus and Comephorus population in the lake Baikal
Bedelbayev A.A. Computer mathematical and biochemical modeling and simulation of the life processes in human organs
Cherevko A.A., Chupakhin A.P., Khe A.K., Vorontsova E.A., Fedorova Y.A., Krivoshapkin A.L., Seleznev P.A. Unsteady hemodynamic simulation of cerebral aneurysms stenting
Chernykh I.G., Kabanikhin S.I., Voronov D.A. CHEMPAK software package: numerical modeling of direct and inverse pharmacokinetics problems
Mikhailova A.V., Cherevko A.A., Chupakhin A.P., Krivoshapkin A.L., Orlov K.Y. Identification of based on experimental clinical data hemodynamic model
Danilov A. A., Kramarenko V. K., Salamatova V. Yu., Yurova A. S. High resolution computational models for bioelectric impedance analysis
Dobroserdova T.K. Numerical simulation of blood flow in the vascular network with pathologies or implants
Doronicheva A.V. Canny algorithm in biomedical images analysis
Gamilov T.M., Simakov S.S. 1D Modelling of different time regimes of enhanced external counterpulsation
Ilyin A.I., Kabanikhin S.I., Krivorotko O.I. The identification and refinement of parameters of mathematical models in immunology
Ivanov Y.A., Pryamonosov R. Patient specific reconstruction of vascular network for hemodynamic modeling
Karacaören B. Dynamic association mapping based on random walk model using simulated QTLMAS data set
Kazantsev F.V., Akberdin I.R., Podkolodnyy N.L., Likhoshvai V.A. Gene networks modeling_ specification language
Kel’manov A. On some analysis, recognition and classification problems of biometrical sequences in a connection with combinatorial optimization problems
Koloskov G., Asmanova N., Ilin A.I. Application of a biexponential form of two-compartment pharmacokinetic models
Konokhova A.I., Gilev K.V., Strokotov D.I., Yurkin M.A., Maltsev V.P. The solution of the inverse light-scattering problem for precise morphological characterization of milk fat globules
Kramarenko V.K. User interfaces for mathematical models, based on human anatomy
Krasnobaeva L.A., Yakushevich L.V. Rotational dynamics of bases in the gene coding interferon alpha 17 (ifna17)
Lenskiy S.V., Lenskaya T.I. Power law for rank distribution of gene density in human genome projects
Levichev A., Palyanov A. On a modification of the theoretical basis of the Penrose-Hameroff model of consciousness
Medvedev A.Ye. Equation of state of blood flows in small vessels
Moskalensky A.E., Strokotov D.I., Yurkin M.A. and Maltsev V.P. Characterization of blood platelets solving the inverse light-scattering problem with pre-computed interpolating set
Mustafin Z.S., Lashin S.A. High perfomance computing computing simulation of evolutionary processes in bacterial communities
Nikitina N.N., Ivashko E.E., Gupta Y., Ludwig R., Möller S. BOINC-based desktop grid infrastructure for virtual drug screening
Petunin D., Intel® Cilk™ Plus – data parallelism and vectorization in С/C++ programs
Polshchitsin A.A., Nekrasov V.M., Chernyshev A.V., and Maltsev V.P. Solution of inverse immunoagglutination kinetics problem for patchy particles with a small number of binding sites
Protsyuk I.V., Grekhov G.A., Tiunov A.V., Fursov M.Y. Shared bioinformatics database within Unipro UGENE
Pyrkova A.Yu., Ivashchenko A.T., Berillo O.A. Modelling of the problem of multiple alignment of the nucleotide sequences and dendrogram construction
Salamatova V.Yu. Modelling of soft tissues deformation. Alternative approaches
Shishlenin M.A. Continuation of the acoustic field in tomography
Ilyin A.I. , Kabanikhin S.I., Voronov D.A. Numerical solutions of inverse problem of pharmacokinetics. Identifiability of compartmental models
Danilov A.A., Yurova A.S. Patient specific 3D models_ some generation techniques
Troeglazova T.S., Baishibaev D.Ja., Penenko A.V., Nikolaev S.V., Zubairova U. On a parallel algorithm for morphogene diffusion-reaction processes simulation on a 2D cell ensemble
Vitvitsky A.A. Computer simulation of self-organization in the bacterial MinCDE syste

Poster

Akinshin A.A., Bukharina T.A., Furman D.P., Golubyatnikov V.P. An extended model of D. melanogaster macrochaete morphogenesis gene network
Barlukova A., Honoré S., Hubert F., Petit M. Dynamic instabilities of microtubules
Bukharin K.V., Lavryushev Ya.S., Lashin S.A. Social interactions in communities of conformists and non-conformists a cellular automaton model
Cherevko A.A., Chupakhin A.P., Yanchenko А.А., Krivoshapkin A.L., Orlov K.U. Unsteady hemodynamic simulation of cerebral aneurysms stenting
Fomin E.S. Reconstruction cyclic sequences from their circular distances multiset
Kiselev I.N., Kolpakov F.A. BioUML: Plugin for population-based modeling
Kogai V.V., Fadeev S.I., Khlebodarova T.M., Likhoshvai V.A. Complex dynamics in systems of alternative mRNA splicing: a mathematical model
Maltseva S.V., Akulov A.E., Derevtsov E.Yu., Cherevko A.A., Chupakhin A.P., Khe A.K. Reconstrucrion of the mouse brain vascular net according to the data of high-field MRI-scanner
Mikhaylova A.V., Cherevko A.A., Chupahin A.P., Krivoshapkin A.L., K.U. Orlov Construction of the hemodynamic model based on clinical data: inverse problem
Nikolaev S.V., Golushko S.K. A structural mechanics model for atomic force microscopy-based indentation test of epidermal plant cells
Nizolenko L.Ph., Bachinsky A.G. A Universal model of the epidemics caused by special pathogens: a tool for epidemiologist
Palyanov A., Khayrulin S. Sibernetic: novel approach to realistic modeling of invertebrates biomechanics
Pyrkova A.Yu., Ivashchenko A.T., Berillo O.A. Parallelization of algorithm of prediction of miRNA binding sites in mRNA on the cluster computing platform
Shitova M.V., Khokhlov Y.N., Nikiforov A.I., Sherbakov D.Y., Zhivotovsky L.A. Microsatellite variation to compare migration scenarios and demographic processes in populations chum salmon northern range
Sviridova N.V., Vlasenko V.D. Individual modelling of hemodynamic processes in cardiovascular system based on peripheral arterial pulsation

TEXT-MINING AND INTELLIGENT ANALYSIS OF KNOWLEDGE IN DATABASES
Oral

Keynote talks

King R. To be announced
Soldatova L. To be announced

Oral presentations

Antonets D.V., Grudin D.S. Using novel Generic String kernel to build pan-specific MHC class I peptide binding prediction tool
Berikov V.B. Centroid-based ensemble of k-means for big data clustering
Gilev K.V., Yurkin M.A., Chernyshev A.V., Maltsev V.P. Solution of the inverse light-scattering problem for characterization of red blood cells
Hofestaedt R.M. Computation of drug interactions and side effects
Ivanisenko V.A., Saik O.V., Tiys E.S., Ivanisenko T.V., Demenkov P.S. ANDSystem: associative network discovery system for automated literature mining in the area of biology
Bazaikin Ya.V., Chupakhin A. P., Cherevko A.A., Khe A.K. Application of the methods of persistent homology to clinical data analysis
Titov I.I., Blinov A.A., Rudnichenko K.A., Krutov P.V., Kazantsev A.L., Kulikov A.I. NetInference: the computer tools for analysis and visualization of networks structure, dynamics and evolution

Poster

Kolosov M.S., Brovchenko P.P. Inferring hypotheses on protein-protein interactions during experimental treatment
Martynovich V.V., Vityaev E.E. Probabilistic formal concepts with negation
Maslov P.P., Berikov V.B. Application of Bayesian methods to the problem of classification of natural language texts
Medvedev A.N. Community structure of web-graphs of academic institutions
Polyakova G.L. Logical-and-probability simulation model of data analysis
Polyakova G.L. Logical-and-probability simulation model of influence of the climatic factors
Romanov D. Dotolog — dot plot analyzation tool
Saik O.V., Demenkov P.S., Ivanisenko V.A. Database of frame models of genetic regulation of the metabolic processes associated with diseases
Sukhotin A.M. Methods of the intellectual analysis of data in natural sciences and alternative analysis